biostudies-arrayexpressNicolas GermainHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15359Recapitulate the myeloid sarcoma gene expression using Gelma hydrogels in leukemic cell lines RNA-seq was performed onleukemic cell lines K562, Molm-13, PL-21, OCI-AML under two conditions (GelMA and control) to assess differential gene expression related to phenotype.biostudies-arrayexpressSample Collection - Cell lines were analyzed after 15 days of culture in suspension. Cells within GelMA 5% hydrogels were collected after dissociation with collagenase type I. All samples were stored at −80 °C until RNA extraction.Library Construction - RNA libraries were prepared using the AccuraCode RNA-Seq Kit (Cat. no. 10710174, Singleron Biotechnologies GmbH) following the manufacturer’s instructions. Polyadenylated mRNA was isolated using AccuraCode beads (Cat. no. 1200030080). cDNA was synthesized with sample-specific barcodes and unique molecular identifiers (UMIs), pooled, and amplified to construct sequencing libraries.Sequencing - Sequencing was performed on an Illumina NovaSeq X platform using paired-end 150 bp reads, following the manufacturer’s protocol.Nucleic Acid Extraction - Total RNA was extracted using the Quick-RNA Microprep Kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s protocol. RNA quantity and purity were assessed with a NanoDrop spectrophotometer (260/280 and 260/230 ratios), and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer with an RNA 6000 Nano Kit. Only samples with RNA Integrity Number (RIN) greater than 7 were retained for library preparationOrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw reads were demultiplexed, trimmed, and aligned to the human GRCh38 reference genome using STAR. Read counts were generated using featureCounts and normalized using the DESeq2 median-of-ratios method.UnknownTranscriptomicsGenomicsProteomicsMicroprep kitIllumina NovaSeq Xaccuracode RNA-seq KitRNA-seq of coding RNAHomo sapiensNicolas GermainfalseTranscriptome profiling of myeloid cell lines in Gelatin Methacrylate HydrogelsRecapitulate the myeloid sarcoma gene expression using Gelma hydrogels in leukemic cell lines RNA-seq was performed onleukemic cell lines K562, Molm-13, PL-21, OCI-AML under two conditions (GelMA and control) to assess differential gene expression related to phenotype.2025-09-01T00:00:00Z2025-09-01T01:02:27.514Z2025-07-14T13:37:21.264ZE-MTAB-15359ERP176757EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184